Cylinder meshes and boundaries
This is caused by the Subdivision modifier.
It interpolates the spacing between edges, and the subdivided geometry is slightly moved.
The same thing is causing the distortion when adding cuts with knife-project. You're effectivelly adding loopcuts, which limits the stretching.
These are your options:

Add a crease to the edge
Make the geometry evenly spaced on the object
Add a loopcut on both sides of the edge
Split the edge using Edge split modifier